It would be quite nice to have a built in file manager for the mission editor. So you can edit your common files such as the init.sqf, description.ext, straight from the game.
Another little feature that would be good, is easily making empty sqf/ext/sqm files etc.
Also, with it being in-game, you could have the 'auto-correct code' that init boxes on units have already, so when writing code, you have all the commands already set out for you.